• Work In Progress! - - -

We continuously review and integrate the old iMAP[1] with Snakemake and GitHub actions to facilitate reproducible microbiome data analysis!



General Overview


We envision to keep fostering on continuous integration and development of highly reproducible workflows.


Snakemake rule-graph

  • Typically the snakemake workflow is defined by specifying rules.
  • The rule-graph graphically shows the input-output files.
  • The snakemake is capable of automatically determining the dependencies between the rules and creates a dot-like DAG (Directed Acyclic Graph).



IMAP-PART3: Snakemake workflow



Screenshot of interactive snakemake report

The snakemake html report can be viewed using any compartible browser, such as chrome to explore more on the workflow and the associated statistics. You will be able to close the left bar to get a better view of the dispaly.



Preliminary OTU Analysis using Mothur

First initiate mothur then run the following commands on mothur cli to generate downstream input data.

Appendix




References

[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4
[2]
Köster, J., Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., … Nahnsen, S. (2021). Sustainable data analysis with snakemake. F1000Research, 10. https://doi.org/10.12688/f1000research.29032.2
[3]
Snakemake. (2023). Snakemake. Retrieved from https://snakemake.readthedocs.io/en/stable
[4]
Close, W. L. (2020). Mothur 16S v4 analysis pipeline. Retrieved from https://github.com/wclose/mothurPipeline